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. 2012 Jun 14:12:86.
doi: 10.1186/1471-2148-12-86.

Variation of presence/absence genes among Arabidopsis populations

Shengjun Tan  1 , Yan Zhong, Huan Hou, Sihai Yang, Dacheng Tian
Affiliations

Variation of presence/absence genes among Arabidopsis populations

Shengjun Tan et al. BMC Evol Biol. .

Abstract

Background: Gene presence/absence (P/A) polymorphisms are commonly observed in plants and are important in individual adaptation and species differentiation. Detecting their abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms in a given species. The recently sequenced 80 Arabidopsis genomes provide an opportunity to address these questions.

Results: By systematically investigating these accessions, we identified 2,407 P/A genes (or 8.9%) absent in one or more genomes, averaging 444 absent genes per accession. 50.6% of P/A genes belonged to multi-copy gene families, or 31.0% to clustered genes. However, the highest proportion of P/A genes, outnumbered in singleton genes, was observed in the regions near centromeres. In addition, a significant correlation was observed between the P/A gene frequency among the 80 accessions and the diversity level at P/A loci. Furthermore, the proportion of P/A genes was different among functional gene categories. Finally, a P/A gene tree showed a diversified population structure in the worldwide Arabidopsis accessions.

Conclusions: An estimate of P/A genes and their frequency distribution in the worldwide Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes, by which individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.

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Figures

Figure 1
Figure 1
Distribution of P/A frequencies among 80 Arabidopsis accessions. (A) Number of P/A genes vs. absent allele frequency. (B) Expected increase of P/A genes relative to the number of sampled accessions, based on a random sampling model. Each datapoint represents an average number of P/A genes for 10000 random simulation samples, and the 95% confidence intervals were also indicated. For example, when 4 accessions are sampled, 919 absent genes are expected.
Figure 2
Figure 2
Co-variation between absent allele frequency and nucleotide diversity (A) or gene length (B).
Figure 3
Figure 3
The reconciled tree. This tree was viewed as the evolved P/A tree inside the accession tree. The accession tree was shown in blue and the P/A tree in black. At the edges of branches were the accession names, countries and 8 regions where they were sampled. Most of the P/A tree vertices matched the accession tree vertices (dark blue ellipses) particularly in each geographic clade, which meant the P/A polymorphic pattern was associated with individual variation.
Figure 4
Figure 4
Distributions of P/A genes on chromosomes. The x-axis represents the physical distance (Mb) on the chromosome. The y-axis represents the proportion of P/A genes for each Mb of chromosomal length. The thick black bar represents the centromeric region.
Figure 5
Figure 5
Distribution of P/A genes in different functional categories. The y-axis on the right is the number of genes in each category and the x-axis is the proportion of P/A genes.
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